You have both hills and urban areas blocking about the whole east side of San Francisco Bay. Hard for me to imagine being able to get through that. And further north you've got the Central Valley.
I'm not sure how hills or urban areas block the ability to canoe... Waterways always are locally low and canoe trips on rivers will typically have hills on either side of you. And I've been on plenty of canoe trips that went through the downtown of a city. Most older cities are built in some place navigable by boat.
The parent was asking about getting down to the SF Bay from somewhere in Sierras. I'd have to study a map in detail but I doubt there are much in the way of east/west routes in that area. Also, while there are navigable waterways in cities they tend to be very limited. There's often one river in older cities that flows through the center somewhere.
It really depends on the watersheds. You can get to Boston from pretty far north but you would have to cheat by going down the coast from the mouth of the Merrimack River which I think captures all the rivers in southern NH/northern MA.
San Francisco owes its growth as a city to the fact that the Bay provides a connection between the Sierras (and their goldfields) and the Pacific Ocean.
Regarding Boston, the interesting thing is that it used to be connected to the Merrimack via the Middlesex Canal. My understanding is that this is silted up now (which you presumably already know) but it shows how many more connections we used to have.
There are many dams and gigantic underground pipes that carry the water through the area. It works fine for the water but not for kayakers. For example the Briones Reservoir is upstream of the San Pablo Reservoir connected by huge gravity-powered pipes under the mountains between them. They are in fact redoing them right now.
There are a significant number of canal systems to the east of the bay. I have no where boating is allowed, but the ones we frequently drive past are ~100 feet wide and extend at least out to Stockton and Sacramento. I have no clue if you can get past those cities, though.
There's no blockage - in fact oceangoing cargo ships can travel all the way to the Port of Sacramento, thanks to a thirty-foot-deep channel maintained by the Corps of Engineers.
Looking at a map more closely I don't know how much is practical in a canoe, but the answer to up thread is probably however far you can up towards Lake Tahoe then down through Folsom Lake to (most of the way?) to Sacramento then Stockton (or just directly to the bay) and probably to the Bay from there.
Not sure you can do the equivalent further south but it looks like you could do a lot of it that way--at least in theory.
